Season short ribs all over with salt and pepper and heat oil in a large Dutch oven over medium high. Working in batches, sear short ribs on all sides, then remove to a plate.
Reduce heat to medium and stir in onion, scraping the bottom of the pot. Cook for 2 minutes, then add carrots and continue to cook for 5 minutes, until carrot is softened. Add the garlic and cook another 30 seconds or so, until fragrant. Stir in tomato paste until well mixed.
Add red wine, beef stock, bay leaves and thyme, and stir well. Arrange short ribs in pot, making sure as much of the meat is submerged as possible. Cover, place in the oven, and cook for 3 hours.
Carefully remove short ribs from the pot (if you want to serve with the bone intact), place on a platter and tent with foil.
Strain the liquid in the pot to remove solids. Set on the stove over medium heat and simmer until reduced by half, adding salt or pepper if needed. Serve short ribs with sauce spooned on top.